Modifying /usr/local/apache/conf/httpd.conf directly for the VirtualHost sections will not be maintained at all. This is indicated above each one, including the default VHost for the server's hostname:

# DO NOT EDIT. AUTOMATICALLY GENERATED. IF YOU NEED TO MAKE A CHANGE PLEASE USE THE INCLUDE FILES.

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If you wish to modify that default entry, you'd do so in /var/cpanel/userdata/nobody/host.domain.com where host.domain.com is the server's hostname. Here's what it looks like: